From 4a048d8f6f70029141ffe4b6630c5eff4ba672f0 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 15 Mar 2017 09:46:01 +0100 Subject: Static documentation except articles rebuilt by pkgdown --- docs/reference/DFOP.solution.html | 9 ++- docs/reference/Extract.mmkin.html | 11 ++-- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 9 ++- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 9 ++- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 9 ++- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 9 ++- docs/reference/FOCUS_2006_datasets.html | 9 ++- docs/reference/FOMC.solution.html | 7 ++- docs/reference/HS.solution.html | 7 ++- docs/reference/IORE.solution.html | 7 ++- docs/reference/SFO.solution.html | 7 ++- docs/reference/SFORB.solution.html | 7 ++- docs/reference/add_err.html | 9 ++- docs/reference/endpoints.html | 9 ++- docs/reference/geometric_mean.html | 7 ++- docs/reference/ilr.html | 9 ++- docs/reference/mccall81_245T.html | 29 +++++---- docs/reference/mkin_long_to_wide.html | 9 ++- docs/reference/mkin_wide_to_long.html | 9 ++- docs/reference/mkinerrmin.html | 9 ++- docs/reference/mkinfit.html | 83 ++++++++++++++------------ docs/reference/mkinmod.html | 11 +++- docs/reference/mkinparplot.html | 9 ++- docs/reference/mkinplot.html | 6 +- docs/reference/mkinpredict.html | 15 +++-- docs/reference/mkinresplot.html | 6 +- docs/reference/mkinsub.html | 9 ++- docs/reference/mmkin.html | 13 ++-- docs/reference/plot.mkinfit.html | 9 ++- 29 files changed, 238 insertions(+), 113 deletions(-) diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index ed30ee50..bad6dd57 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -6,7 +6,8 @@ -Double First-Order in Parallel kinetics — DFOP.solution • mkin + + — DFOP.solution • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Double First-Order in Parallel kinetics

    +

    +

    diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 4ef3bb00..0131342a 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -71,6 +71,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -239,7 +242,7 @@ #> #> $time #> user system elapsed -#> 0.064 0.000 0.065 +#> 0.068 0.000 0.066 #> #> $mkinmod #> <mkinmod> model generated with @@ -428,7 +431,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5ce33e0> +#> <environment: 0x3b9eeb8> #> #> $cost_notrans #> function (P) @@ -450,7 +453,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5ce33e0> +#> <environment: 0x3b9eeb8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -513,7 +516,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Dec 8 07:56:34 2016" +#> [1] "Wed Mar 15 09:44:44 2017" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index df8280d7..fff99b6c 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -6,7 +6,8 @@ -Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin + + — FOCUS_2006_DFOP_ref_A_to_B • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)

    +

    +

    diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 6132388f..5c9feb23 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -6,7 +6,8 @@ -Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin + + — FOCUS_2006_FOMC_ref_A_to_F • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)

    +

    +

    diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 86b071cf..8ccbd86a 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -6,7 +6,8 @@ -Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkin + + — FOCUS_2006_HS_ref_A_to_F • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Results of fitting the HS model to Datasets A to F of FOCUS (2006)

    +

    +

    diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index b2d199d3..263b9b31 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -6,7 +6,8 @@ -Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkin + + — FOCUS_2006_SFO_ref_A_to_F • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Results of fitting the SFO model to Datasets A to F of FOCUS (2006)

    +

    +

    diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index cde972b7..71dbe761 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -6,7 +6,8 @@ -Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin + + — FOCUS_2006_datasets • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Datasets A to F from the FOCUS Kinetics report from 2006

    +

    +

    diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 932935b4..8d0ed869 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -6,7 +6,7 @@ -First-Order Multi-Compartment kinetics — FOMC.solution • mkin + First-Order Multi-Compartment kinetics — FOMC.solution • mkin @@ -71,6 +71,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +95,7 @@
    -

    First-Order Multi-Compartment kinetics

    +

    First-Order Multi-Compartment kinetics

    diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 2d0b6e4f..b8e6f524 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -6,7 +6,7 @@ -Hockey-Stick kinetics — HS.solution • mkin + Hockey-Stick kinetics — HS.solution • mkin @@ -71,6 +71,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +95,7 @@
    -

    Hockey-Stick kinetics

    +

    Hockey-Stick kinetics

    diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 35e01039..8caef574 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -6,7 +6,7 @@ -Indeterminate order rate equation kinetics — IORE.solution • mkin + Indeterminate order rate equation kinetics — IORE.solution • mkin @@ -71,6 +71,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +95,7 @@
    -

    Indeterminate order rate equation kinetics

    +

    Indeterminate order rate equation kinetics

    diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 3fa6d1d4..e2c93102 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -6,7 +6,7 @@ -Single First-Order kinetics — SFO.solution • mkin + Single First-Order kinetics — SFO.solution • mkin @@ -71,6 +71,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +95,7 @@
    -

    Single First-Order kinetics

    +

    Single First-Order kinetics

    diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index d4661cfd..4a73ba9e 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -6,7 +6,7 @@ -Single First-Order Reversible Binding kinetics — SFORB.solution • mkin + Single First-Order Reversible Binding kinetics — SFORB.solution • mkin @@ -71,6 +71,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +95,7 @@
    -

    Single First-Order Reversible Binding kinetics

    +

    Single First-Order Reversible Binding kinetics

    diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index edced046..aab42f56 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -6,7 +6,8 @@ -Add normally distributed errors to simulated kinetic degradation data — add_err • mkin + + — add_err • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Add normally distributed errors to simulated kinetic degradation data

    +

    +

    diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 38a6a400..4145825a 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -6,7 +6,8 @@ -Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin + + — endpoints • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Function to calculate endpoints for further use from kinetic models fitted with mkinfit

    +

    +

    diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 03b9f54b..828ec471 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -6,7 +6,7 @@ -Calculate the geometric mean — geometric_mean • mkin + Calculate the geometric mean — geometric_mean • mkin @@ -71,6 +71,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +95,7 @@
    -

    Calculate the geometric mean

    +

    Calculate the geometric mean

    diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 85f203ed..4262fa81 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -6,7 +6,8 @@ -Function to perform isometric log-ratio transformation — ilr • mkin + + — ilr • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Function to perform isometric log-ratio transformation

    +

    +

    diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 123af096..4fa32b30 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -6,7 +6,8 @@ -Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin + + — mccall81_245T • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Datasets on aerobic soil metabolism of 2,4,5-T in six soils

    +

    +

    @@ -128,10 +133,10 @@ phenol = list(type = "SFO", to = "anisole"), anisole = list(type = "SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
    #> Warning: Optimisation by method Port did not converge. -#> Convergence code is 1
    summary(fit.1, data = FALSE)
    #> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:56:42 2016 -#> Date of summary: Thu Dec 8 07:56:42 2016 +#> Convergence code is 1
    summary(fit.1, data = FALSE)
    #> mkin version: 0.9.45.1 +#> R version: 3.3.3 +#> Date of fit: Wed Mar 15 09:44:52 2017 +#> Date of summary: Wed Mar 15 09:44:52 2017 #> #> #> Warning: Optimisation by method Port did not converge. @@ -146,7 +151,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 590 model solutions performed in 3.474 s +#> Fitted with method Port using 590 model solutions performed in 3.519 s #> #> Weighting: none #> @@ -223,10 +228,10 @@ fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), parms.ini = c(k_phenol_sink = 0), fixed_parms = "k_phenol_sink", quiet = TRUE) - summary(fit.2, data = FALSE)
    #> mkin version: 0.9.44.9000 -#> R version: 3.3.2 -#> Date of fit: Thu Dec 8 07:56:44 2016 -#> Date of summary: Thu Dec 8 07:56:44 2016 + summary(fit.2, data = FALSE)
    #> mkin version: 0.9.45.1 +#> R version: 3.3.3 +#> Date of fit: Wed Mar 15 09:44:54 2017 +#> Date of summary: Wed Mar 15 09:44:54 2017 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -236,7 +241,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.44 s +#> Fitted with method Port using 246 model solutions performed in 1.449 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index af7daf7a..9b37726e 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -6,7 +6,8 @@ -Convert a dataframe from long to wide format — mkin_long_to_wide • mkin + + — mkin_long_to_wide • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Convert a dataframe from long to wide format

    +

    +

    diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 75417aec..378d3691 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -6,7 +6,8 @@ -Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin + + — mkin_wide_to_long • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Convert a dataframe with observations over time into long format

    +

    +

    diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index a69920fd..97616a41 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -6,7 +6,8 @@ -Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin + + — mkinerrmin • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Calculate the minimum error to assume in order to pass the variance test

    +

    +

    diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 3dd701d3..01c930e2 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -6,7 +6,8 @@ -Fit a kinetic model to data with one or more state variables — mkinfit • mkin + + — mkinfit • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Fit a kinetic model to data with one or more state variables

    +

    +

    @@ -372,17 +377,17 @@

    Examples

    # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
    #> mkin version:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:56:46 2016 
-#> Date of summary: Thu Dec  8 07:56:46 2016 
+summary(fit)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:44:56 2017 
+#> Date of summary: Wed Mar 15 09:44:56 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.145 s
+#> Fitted with method Port using 64 model solutions performed in 0.146 s
 #> 
 #> Weighting: none
 #> 
@@ -451,7 +456,7 @@
   m1 = mkinsub("SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    # Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
    #>    user  system elapsed 
-#>   1.172   1.232   0.904 
    coef(fit)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   1.216   1.268   0.942 
    coef(fit)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
    endpoints(fit)
    #> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -528,7 +533,7 @@
 #> Model cost at call  152 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>    user  system elapsed 
-#>   0.712   0.044   0.709 
    coef(fit.deSolve)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   0.712   0.040   0.703 
    coef(fit.deSolve)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
    endpoints(fit.deSolve)
    #> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -569,10 +574,10 @@
 # Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
                       m1 = mkinsub("SFO"), use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(f.noweight)
    #> mkin version:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:56:57 2016 
-#> Date of summary: Thu Dec  8 07:56:57 2016 
+summary(f.noweight)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:07 2017 
+#> Date of summary: Wed Mar 15 09:45:07 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -580,7 +585,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 185 model solutions performed in 0.77 s
+#> Fitted with method Port using 185 model solutions performed in 0.753 s
 #> 
 #> Weighting: none
 #> 
@@ -690,10 +695,10 @@
 #>   100       m1    33.13 3.198e+01  1.148e+00
 #>   120       m1    25.15 2.879e+01 -3.640e+00
 #>   120       m1    33.31 2.879e+01  4.520e+00
    f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
-summary(f.irls)
    #> mkin version:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:56:59 2016 
-#> Date of summary: Thu Dec  8 07:56:59 2016 
+summary(f.irls)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:09 2017 
+#> Date of summary: Wed Mar 15 09:45:09 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -701,7 +706,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 486 model solutions performed in 2.019 s
+#> Fitted with method Port using 486 model solutions performed in 2.091 s
 #> 
 #> Weighting: none then iterative reweighting method obs
 #> 
@@ -811,10 +816,10 @@
 #>   100       m1    33.13 3.199e+01  1.140e+00 2.722
 #>   120       m1    25.15 2.881e+01 -3.659e+00 2.722
 #>   120       m1    33.31 2.881e+01  4.501e+00 2.722
    f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
-summary(f.w.mean)
    #> mkin version:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:57:00 2016 
-#> Date of summary: Thu Dec  8 07:57:00 2016 
+summary(f.w.mean)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:10 2017 
+#> Date of summary: Wed Mar 15 09:45:10 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -822,7 +827,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.65 s
+#> Fitted with method Port using 155 model solutions performed in 0.661 s
 #> 
 #> Weighting: mean
 #> 
@@ -933,10 +938,10 @@
 #>   120       m1    25.15 28.824128  -3.674128
 #>   120       m1    33.31 28.824128   4.485872
    f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value",
                      quiet = TRUE)
-summary(f.w.value)
    #> mkin version:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:57:01 2016 
-#> Date of summary: Thu Dec  8 07:57:01 2016 
+summary(f.w.value)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:11 2017 
+#> Date of summary: Wed Mar 15 09:45:11 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -944,7 +949,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.713 s
+#> Fitted with method Port using 174 model solutions performed in 0.724 s
 #> 
 #> Weighting: manual
 #> 
@@ -1055,10 +1060,10 @@
 errors <- c(parent = 2, m1 = 1)
 dw$err.man <- errors[FOCUS_2006_D$name]
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
-summary(f.w.man)
    #> mkin version:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:57:02 2016 
-#> Date of summary: Thu Dec  8 07:57:02 2016 
+summary(f.w.man)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:12 2017 
+#> Date of summary: Wed Mar 15 09:45:12 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1066,7 +1071,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 316 model solutions performed in 1.322 s
+#> Fitted with method Port using 316 model solutions performed in 1.31 s
 #> 
 #> Weighting: manual
 #> 
@@ -1177,10 +1182,10 @@
 #>   120       m1    25.15 28.760615  -3.610615   2
 #>   120       m1    33.31 28.760615   4.549385   2
    f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE,
                        reweight.method = "obs")
-summary(f.w.man.irls)
    #> mkin version:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:57:05 2016 
-#> Date of summary: Thu Dec  8 07:57:05 2016 
+summary(f.w.man.irls)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:15 2017 
+#> Date of summary: Wed Mar 15 09:45:15 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1188,7 +1193,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 648 model solutions performed in 2.818 s
+#> Fitted with method Port using 648 model solutions performed in 2.766 s
 #> 
 #> Weighting: manual then iterative reweighting method obs
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 1044af6b..1343abcc 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -6,7 +6,8 @@
 
 
 
-Function to set up a kinetic model with one or more state variables — mkinmod • mkin
+
+ — mkinmod • mkin
 
 
 
@@ -71,6 +72,9 @@
       Performance benefit by using compiled model definitions in mkin
     
   
+
+
  • 
+  News
 
    • 
       
       
@@ -92,7 +96,8 @@
       
    
   
    
     
    
-    
    Function to set up a kinetic model with one or more state variables
    
+    
    
+
    
     
    
 
     
@@ -188,7 +193,7 @@
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
    #> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file386742883b12.c 2> file386742883b12.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file2ac5b2884c1.c 2> file2ac5b2884c1.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 744de866..0682211b 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -6,7 +6,8 @@
 
 
 
-Function to plot the confidence intervals obtained using mkinfit — mkinparplot • mkin
+
+ — mkinparplot • mkin
 
 
 
@@ -71,6 +72,9 @@
       Performance benefit by using compiled model definitions in mkin
     
   
+
+
  • 
+  News
 
    • 
       
       
@@ -92,7 +96,8 @@
       
    
   
    
     
    
-    
    Function to plot the confidence intervals obtained using mkinfit
    
+    
    
+
    
     
    
 
     
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 898b1b9f..fdc61af4 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -6,7 +6,8 @@
 
 
 
-Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin
+
+ — mkinplot • mkin
 
 
 
@@ -95,7 +96,8 @@
       
    
   
    
     
    
-    
    Plot the observed data and the fitted model of an mkinfit object
    
+    
    
+
    
     
    
 
     
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 766b6613..2348d40e 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -6,7 +6,8 @@
 
 
 
-Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin
+
+ — mkinpredict • mkin
 
 
 
@@ -71,6 +72,9 @@
       Performance benefit by using compiled model definitions in mkin
     
   
+
+
  • 
+  News
 
    • 
       
       
@@ -92,7 +96,8 @@
       
    
   
    
     
    
-    
    Produce predictions from a kinetic model using specific parameters
    
+    
    
+
    
     
    
 
     
@@ -290,17 +295,17 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
    #>     time   parent       m1
 #> 201   20 4.978707 27.46227
    #>    user  system elapsed 
-#>   0.012   0.020   0.005 
      system.time(
+#>   0.016   0.016   0.004 
      system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
    #>     time   parent       m1
 #> 201   20 4.978707 27.46227
    #>    user  system elapsed 
-#>   0.000   0.020   0.003 
      system.time(
+#>   0.016   0.004   0.002 
      system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
    #>     time   parent       m1
 #> 201   20 4.978707 27.46227
    #>    user  system elapsed 
-#>   0.032   0.000   0.035
    +#> 0.032 0.000 0.034